Highly Regional Genes: graph-based gene selection for single cell RNA-seq data

Hotspot identifies informative gene modules across modalities of single-cell genomics

(2021) David DeTomaso et al.   Cell Systems

Statistical analysis of spatial expression patterns for spatially resolved transcriptomic studies

(2020) Shiquan Sun et al.   NATURE METHODS

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

Functional interpretation of single cell similarity maps

(2019) David DeTomaso et al.   Nature Communications

Spatial transcriptomic survey of human embryonic cerebral cortex by single-cell RNA-seq analysis

(2018) Xiaoying Fan et al.   CELL RESEARCH

M3Drop: dropout-based feature selection for scRNASeq

(2018) Tallulah S Andrews et al.   BIOINFORMATICS

Dimensionality reduction for visualizing single-cell data using UMAP

(2018) Etienne Becht et al.   NATURE BIOTECHNOLOGY

Reference component analysis of single-cell transcriptomes elucidates cellular heterogeneity in human colorectal tumors

(2017) Huipeng Li et al.   NATURE GENETICS

Massively parallel digital transcriptional profiling of single cells

(2017) Grace X. Y. Zheng et al.   Nature Communications

Heterogeneity in Oct4 and Sox2 Targets Biases Cell Fate in 4-Cell Mouse Embryos

(2016) Mubeen Goolam et al.   CELL

Single-Cell Transcriptome Profiling of Human Pancreatic Islets in Health and Type 2 Diabetes

(2016) Åsa Segerstolpe et al.   Cell Metabolism

Molecular interrogation of hypothalamic organization reveals distinct dopamine neuronal subtypes

(2016) Roman A Romanov et al.   NATURE NEUROSCIENCE

Oligodendrocyte heterogeneity in the mouse juvenile and adult central nervous system

(2016) S. Marques et al.   SCIENCE

Visualization and analysis of gene expression in tissue sections by spatial transcriptomics

(2016) P. L. Stahl et al.   SCIENCE

A Single-Cell Transcriptomic Map of the Human and Mouse Pancreas Reveals Inter- and Intra-cell Population Structure

(2016) Maayan Baron et al.   Cell Systems

Identification of cell types from single-cell transcriptomes using a novel clustering method

(2015) Chen Xu et al.   BIOINFORMATICS

Droplet Barcoding for Single-Cell Transcriptomics Applied to Embryonic Stem Cells

(2015) Allon M. Klein et al.   CELL

Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets

(2015) Evan Z. Macosko et al.   CELL

A survey of human brain transcriptome diversity at the single cell level

(2015) Spyros Darmanis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq

(2015) A. Zeisel et al.   SCIENCE

Genome-wide RNA Tomography in the Zebrafish Embryo

(2014) Jan Philipp Junker et al.   CELL

Spatially resolved transcriptomics and beyond

(2014) Nicola Crosetto et al.   NATURE REVIEWS GENETICS

In situ sequencing for RNA analysis in preserved tissue and cells

(2013) Rongqin Ke et al.   NATURE METHODS

Mouse and computational models link Mlc2v dephosphorylation to altered myosin kinetics in early cardiac disease

(2012) Farah Sheikh et al.   JOURNAL OF CLINICAL INVESTIGATION

CEL-Seq: Single-Cell RNA-Seq by Multiplexed Linear Amplification

(2012) Tamar Hashimshony et al.   Cell Reports

mRNA-Seq whole-transcriptome analysis of a single cell

(2009) Fuchou Tang et al.   NATURE METHODS